Luyao Wang1,2,3, Jin Han3, Kening Lu2, Menglin Li2, Mengtao Gao2, Zeyi Cao3, Ting Zhao3, Xue Chen2, Xiaoyuan Tao3, Quanjia Chen4, Xueying Guan5,6. 1. Engineering Research Centre of Cotton, Ministry of Education / College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, 830052, Urumqi, China. 2. State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China. 3. College of Agriculture and Biotechnology, Zhejiang University, 210058, Hangzhou, Zhejiang, China. 4. Engineering Research Centre of Cotton, Ministry of Education / College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, 830052, Urumqi, China. chqjia@126.com. 5. College of Agriculture and Biotechnology, Zhejiang University, 210058, Hangzhou, Zhejiang, China. xueyingguan@zju.edu.cn. 6. Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Building 11, Yonyou Industrial Park, Yazhou District, Hainan Province, 572025, Sanya, China. xueyingguan@zju.edu.cn.
Abstract
BACKGROUND: An evolutionary model using diploid and allotetraploid cotton species identified 80 % of non-coding transcripts in allotetraploid cotton as being uniquely activated in comparison with its diploid ancestors. The function of the lncRNAs activated in allotetraploid cotton remain largely unknown. RESULTS: We employed transcriptome analysis to examine the relationship between the lncRNAs and mRNAs of protein coding genes (PCGs) in cotton leaf tissue under abiotic stresses. LncRNA expression was preferentially associated with that of the flanking PCGs. Selected highly-expressed lncRNA candidates (n = 111) were subjected to a functional screening pilot test in which virus-induced gene silencing was integrated with abiotic stress treatment. From this low-throughput screen, we obtained candidate lncRNAs relating to plant height and tolerance to drought and other abiotic stresses. CONCLUSIONS: Low-throughput screen is an effective method to find functional lncRNA for further study. LncRNAs were more active in abiotic stresses than PCG expression, especially temperature stress. LncRNA XLOC107738 may take a cis-regulatory role in response to environmental stimuli. The degree to which lncRNAs are constitutively expressed may impact expression patterns and functions on the individual gene level rather than in genome-wide aggregate.
BACKGROUND: An evolutionary model using diploid and allotetraploid cotton species identified 80 % of non-coding transcripts in allotetraploid cotton as being uniquely activated in comparison with its diploid ancestors. The function of the lncRNAs activated in allotetraploid cotton remain largely unknown. RESULTS: We employed transcriptome analysis to examine the relationship between the lncRNAs and mRNAs of protein coding genes (PCGs) in cotton leaf tissue under abiotic stresses. LncRNA expression was preferentially associated with that of the flanking PCGs. Selected highly-expressed lncRNA candidates (n = 111) were subjected to a functional screening pilot test in which virus-induced gene silencing was integrated with abiotic stress treatment. From this low-throughput screen, we obtained candidate lncRNAs relating to plant height and tolerance to drought and other abiotic stresses. CONCLUSIONS: Low-throughput screen is an effective method to find functional lncRNA for further study. LncRNAs were more active in abiotic stresses than PCG expression, especially temperature stress. LncRNA XLOC107738 may take a cis-regulatory role in response to environmental stimuli. The degree to which lncRNAs are constitutively expressed may impact expression patterns and functions on the individual gene level rather than in genome-wide aggregate.
Entities:
Keywords:
Abiotic stress; Conservation; lncRNA function
Authors: Florian A Karreth; Markus Reschke; Anna Ruocco; Christopher Ng; Bjoern Chapuy; Valentine Léopold; Marcela Sjoberg; Thomas M Keane; Akanksha Verma; Ugo Ala; Yvonne Tay; David Wu; Nina Seitzer; Martin Del Castillo Velasco-Herrera; Anne Bothmer; Jacqueline Fung; Fernanda Langellotto; Scott J Rodig; Olivier Elemento; Margaret A Shipp; David J Adams; Roberto Chiarle; Pier Paolo Pandolfi Journal: Cell Date: 2015-04-02 Impact factor: 41.582
Authors: X M Zheng; J Chen; H B Pang; S Liu; Q Gao; J R Wang; W H Qiao; H Wang; J Liu; K M Olsen; Q W Yang Journal: Sci Adv Date: 2019-12-18 Impact factor: 14.136